Onchocerciasis is a neglected tropical disease targeted for elimination using mass drug admin-istration of ivermectin (MDAi). Ivermectin kills the larvae (microfilariae) and causes temporary infertility of female worms. In several regions of sub-Saharan Africa, a sub-optimal response to ivermectin has been identified when microfilariae repopulate the skin earlier than expected. Monitoring changes in mitochondrial haplotypes over the course of MDAi may be useful for identifying how many female worms are contributing to the early-appearing microfilariae. To explore this possibility, we have genotyped microfilariae from people in the Democratic Republic of Congo (DRC) and South Sudan, collected before and after ivermectin treatment. Population genetic analyses of these data indicate that per-person haplotype diversity is lower in the DRC than the South Sudan sample, suggesting that people from the sampling location in South Sudan may be carrying a higher burden of infection.